Variant report

Variant	rs57544538
Chromosome Location	chr9:108521072-108521073
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAL2-3	chr9:108520651-108523036	NONHSAT133827

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10512342	1.00[EUR][1000 genomes]
rs12345407	1.00[EUR][1000 genomes]
rs16924820	1.00[EUR][1000 genomes]
rs16924997	0.83[EUR][1000 genomes]
rs34006675	1.00[EUR][1000 genomes]
rs35232724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57288965	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57694909	1.00[EUR][1000 genomes]
rs58554531	1.00[EUR][1000 genomes]
rs58943241	1.00[EUR][1000 genomes]
rs59271367	1.00[AMR][1000 genomes]
rs59314159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59372367	1.00[AMR][1000 genomes]
rs59747314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6477452	1.00[EUR][1000 genomes]
rs7022006	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7030040	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7047325	1.00[EUR][1000 genomes]
rs73504072	1.00[AMR][1000 genomes]
rs73504080	1.00[AMR][1000 genomes]
rs73504101	1.00[AMR][1000 genomes]
rs73504102	1.00[AMR][1000 genomes]
rs73506304	1.00[AMR][1000 genomes]
rs73506307	1.00[AMR][1000 genomes]
rs73516084	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73518117	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73518124	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73518141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73518160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73518170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73518183	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73520071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73520092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73520094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522055	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522061	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73522067	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7866807	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7873482	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv615116	chr9:108468129-108546438	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv982335	chr9:108520769-108531325	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108513800-108521400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:108514000-108540000	Weak transcription	HSMMtube	muscle
3	chr9:108514800-108521400	Weak transcription	Spleen	Spleen
4	chr9:108515200-108522800	Weak transcription	Left Ventricle	heart
5	chr9:108515200-108545000	Weak transcription	K562	blood
6	chr9:108515200-108560600	Weak transcription	Ovary	ovary
7	chr9:108515400-108523400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:108515400-108536800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:108515600-108522400	Weak transcription	Liver	Liver
10	chr9:108515600-108538600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:108517200-108522000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr9:108517800-108538400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:108520600-108522800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:108520600-108523200	Weak transcription	Pancreas	Pancrea
15	chr9:108520600-108535200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:108520600-108546400	Weak transcription	Fetal Intestine Small	intestine
17	chr9:108521000-108534200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:108521000-108538400	Weak transcription	Primary B cells from cord blood	blood

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